Fred L. Allen

Quantitative trait loci for agronomic and seed quality traits in an F2 and F4:6 soybean population

AbstractMolecular breeding is becoming more practical as better technology emerges. The use of molecular markers in plant breeding for indirect selection of important traits can favorably impact breeding efficiency. The purpose of this research is to identify quantitative trait loci (QTL) on molecular linkage groups (MLG) which are associated with seed protein concentration, seed oil concentration, seed size, plant height, lodging, and maturity, in a population from a cross between the soybean cultivars ‘Essex’ and ‘Williams.’ DNA was extracted from F2 generation soybean leaves and amplified via polymerase chain reaction (PCR) using simple sequence repeat (SSR) markers. Markers that were polymorphic between the parents were analyzed against phenotypic trait data from the F2 and F4:6 generation. For the F2 population, significant additive QTL were Satt540 (MLG M, maturity, r2 = 0.11; height, r2 = 0.04, seed size, r2= 0.06], Satt373 (MLG L, seed size, r2 = 0.04; height, r2 = 0.14), Satt50 (MLG A1, maturity r2 = 0.07), Satt14 (MLG D2, oil, r2 = 0.05), and Satt251 (protein r2 = 0.03, oil, r2 =0.04). Significant dominant QTL for the F2 population were Satt540 (MLG M,height, r2 = 0.04; seed size, r2 = 0.06) and Satt14 (MLG D2, oil, r2 = 0.05). In the F4:6 generation significant additive QTL were Satt239 (MLGI, height, r2 = 0.02 at Knoxville, TN and r2 = 0.03 at Springfield, TN), Satt14 (MLG D2, seed size, r2 = 0.14 at Knoxville, TN), Satt373 (MLG L, protein, r2 = 0.04 at Knoxville, TN) and Satt251 (MLG B1, lodging r2 = 0.04 at Springfield, TN). Averaged over both environments in the F4:6 generation, significant additive QTL were identified as Satt251 (MLG B1, protein, r2 = 0.03), and Satt239 (MLG I, height, r2 = 0.03). The results found in this study indicate that selections based solely on these QTL would produce limited gains (based on low r2 values). Few QTL were detected to be stable across environments. Further research to identify stable QTL over environments is needed to make marker-assisted approaches more widely adopted by soybean breeders.

Switchgrass yield and stand dynamics from legume intercropping based on seeding rate and harvest management

Intercropping legumes may reduce inputs and enhance sustainability of forage and feedstock production, especially on marginal soils. This approach is largely untested for switchgrass (Panicum virgatum L.) production, yet producer acceptance should be high given the traditional use of legumes in forage/agricultural systems. Our objectives were to evaluate three cool-season and two warm-season legumes and their required densities to influence yield and supply nitrogen (N) compared to three inorganic N levels (0, 33, and 66 kg N ha−1 [0, 30, and 60 lb N ac−1]) at three locations in Tennessee (Knoxville [Sequatchie Silt Loam], Crossville [Lilly Loam], and Milan [Loring B2 Series]). Fall of 2010 seeded, cool-season legumes (red clover [Trifolium pratense L.], hairy vetch [Vicia villosa L.], ladino clover [Trifolium repens L.]), arrowleaf clover (Trifolium vesiculosum L.), and a spring of 2011 seeded, warm-season legume (partridge pea [Chamaecrista fasciculate L.]) were interseeded into switchgrass at three (high, medium, and low) seeding rates each in two experiments. Harvest treatments were annual single, postdormancy biofuel (Experiment One) or integrated forage-biofuel (preanthesis and postdormancy; Experiment Two). Year one yield impacts were minimal. During the second harvest year, legumes increased yield versus Year 1; in general, yields for 33 and 67 kg N ha−1 did not differ from those for red clover, hairy vetch, ladino clover, or partridge pea (p < 0.05). Arrowleaf clover yields were not different from 0 kg N ha−1. Forage biomass yields were generally more responsive to legumes (p < 0.05) than the biomass regime. Legume persistence after three years was generally greatest for ladino clover and partridge pea. Forage quality (switchgrass only) in some cases was positively influenced by legume treatments, notably hairy vetch and partridge pea (p < 0.05). Intercropping selected legumes in switchgrass may enhance forage quality and yield while reducing nonrenewable inputs, fertilizer costs, and emissions/runoff to air and groundwater.

Biomass and integrated forage/biomass yields of switchgrass as affected by intercropped cool- and warm-season legumes

Switchgrass (Panicum virgatum L.) has potential as a biofuel feedstock for ethanol production on marginal soils not suitable for row crop production. Further, it is hypothesized that legumes may be interseeded into switchgrass to increase available soil nitrogen (N) and enhance switchgrass yields. Therefore the primary objective was to identify compatible legume species for intercropping with lowland switchgrass and determine if biomass yields and forage quality can be improved. Four cool- and two warm-season legume species were compared to application of 67 and 134 kg N ha−1 (59.8 and 119.6 lb N ac−1) during 2009 and 2010 over a range of soils at three research and education centers in Tennessee. Cool-season legumes were alfalfa (Medicago sativa L.), red clover (Trifolium pratense L.), crimson clover (Trifolium incarnatum L.), and hairy vetch (Vicia villosa L.), and warm-season legumes included Illinois bundle flower (Desmanthus illinoensis L.) and partridge pea (Chamaechrista fasciculata L.). Legumes were evaluated for establishment (plant densities) and their effects on switchgrass yield and forage quality under a one-cut biomass (single, postdormancy biofuel) and an integrated two-cut (biomass/forage [preanthesis]) system. In the one-cut system, switchgrass yields (16.6 Mg ha−1 [6.7 tn ac−1]) from the current recommended rate (67 kg N ha−1 [59.8 lb N ac−1]) exceeded (p < 0.05) legume treatment yields (average 13.5 Mg ha−1 [5.5 tn ac−1]). In the integrated harvest system, switchgrass yields from red (13.4 Mg ha−1 [5.4 tn ac−1]) and crimson clover (12.8 Mg ha−1 [5.2 tn ac−1]) intercrops were not different from 67 kg N ha−1 (14.5 Mg ha−1 [5.9 tn ac−1]). Crude protein levels were greater (p < 0.05) for 134 kg N ha−1 (119.6 lb N ac−1), compared to legume intercrops (except red clover). Partridge pea showed promise as a warm-season legume that can be grown compatibly with switchgrass for up to two years. Therefore, compatible legume-intercrop candidates, such as partridge pea and red clover, may enhance switchgrass yield and forage quality while displacing synthetic N in integrated biofuel/forage systems, but need to be further investigated in efforts to reduce nitrate (NO3) leaching and emissions from fertilizing.

Soybean Seed Amino Acid Content QTL Detected Using the Uni- versal Soy Linkage Panel 1.0 with 1,536 SNPs

1 Current address: Clemson Pee Dee REC, Advanced Plant Technology Center, 2200 Pocket Road, Florence, SC 29506, USA; 2 University of Tennessee, Department of Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN 37996, USA; 3 Monsanto, 140 W. Industrial Drive, Harrisburg, SD 57032, USA; 4 University of Arkansas, Department of Crop, Soil, and Environmental Sciences, Fayetteville, AR 72701, USA; 5 Southern Illinois University, Department of Plant, Soil Science and Agricultural Systems, 1205 Lincoln Drive, Carbondale, IL 62901, USA; 6 Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center – West, USDA, ARS, Beltsville, MD 20705, USA; 7 Current address: DuPont Pioneer, 8305 NW 62nd Ave., PO Box 7060, Johnston, IA 50131-7060, USA.

Comparison of Near Infrared Reflectance Spectroscopy with Combustion and Chemical Methods for Soil Carbon Measurements in Agricultural Soils

ABSTRACT As interest in soil organic carbon (SOC) dynamics increases, so do needs for rapid, accurate, and inexpensive methods for quantifying SOC. Objectives were to i) evaluate near infrared reflectance (NIR) spectroscopy potential to determine SOC and soil organic matter (SOM) in soils from across Tennessee, USA; and ii) evaluate potential upper limits of SOC from forest, pasture, no-tillage, and conventional tilled sites. Samples were analyzed via dry-combustion (SOC), Walkley–Black chemical SOM, and NIR. In addition, the sample particle size was classified to give five surface roughness levels to determine effects of particle size on NIR. Partial least squares regression was used to develop a model for predicting SOC as measured by NIR by comparing against SOM and SOC. Both NIR and SOM correlated well (R2 > 0.9) with SOC (combustion). NIR is therefore considered a sufficiently accurate method for quantifying SOC in soils of Tennessee, with pasture and forested systems having the greatest accumulations.Abbreviations SOC, soil organic carbon; NIR, Near Infrared Reflectance Spectroscopy; MTREC, Middle Tennessee Research and Education Center; RECM, Research and Education Center at Milan; PREC, Plateau Research and Education Center; PLS, Partial least squares.

Global meta-analysis reveals agro-grassland productivity varies based on species diversity over time

Ecological research suggests increased diversity may improve ecosystem services, as well as yield stability; however, such theories are sometimes disproven by agronomic research, particularly at higher diversity levels. We conducted a meta-analysis on 2,753 studies in 48 articles published over the last 53 years to test: if biological N2 fixation (BNF) supplies adequate nitrogen (N) for plant growth relative to synthetic fertilizers; how crop physiological traits affect legume-grass symbiosis; and, how cultural practices affect BNF over a range of soils and climates overtime (in polycultures versus sole grasslands). Globally, net primary productivity (NPP; total aboveground production response of grass and legume in higher-diversity treatments) increased 44% via legume associations relative to sole grass controls (including both with and without N fertilizer). Several moderating variables affected NPP including: (i) plant photosynthetic pathway (mixtures of C3 grasses resulted in a 57% increase in NPP, whereas mixtures of C4 grasses resulted in a 31% increase; similarly cool-season legumes increased NPP 52% compared to a 27% increase for warm-season legumes relative to grasslands without diversity); (ii) legume life cycle [NPP response for perennial legume mixtures was 50% greater than sole grass controls, followed by a 28% increase for biennial, and a 0% increase for annual legumes)]; and, (iii) species richness (one leguminous species in a grassland agroecosystem resulted in 52% increase in NPP, whereas >2 legumes resulted in only 6% increases). Temporal and spatial effect sizes also influenced facilitation, considering facilitation was greatest (114% change) in Mediterranean climates followed by oceanic (84%), and tropical savanna (65%) environments; conversely, semiarid and subarctic systems had lowest Rhizobium-induced changes (5 and 0% change, respectively). Facilitation of grass production by legumes was also affected by soil texture. For example, a 122% NPP increase was observed in silt clay soils compared to 14% for silt loam soils. Niche complementarity effects were greatest prior to 1971 (61% change), compared to recent studies (2011–2016; -7% change), likely owing to reduced global sulfur deposition and increased ambient temperatures overtime. These historical trends suggest potential for legume intercrops to displace inorganic-N fertilizer and sustainably intensify global NPP. Results herein provide a framework for ecologists and agronomists to improve crop diversification systems, refine research goals, and heighten BNF capacities in agro-grasslands.

Crop Rotations and Poultry Litter Affect Dynamic Soil Chemical Properties and Soil Biota Long Term

Dynamic soil chemical interactions with conservation agricultural practices and soil biota are largely unknown. Therefore, this study aims to quantify long-term (12-yr) impacts of cover crops, poultry litter, crop rotations, no-tillage, and their interactions on dynamic soil properties and to determine their relationships with nutrient cycling, crop yield, and soil biodiversity (soil microbial and earthworm communities). Main effects were 13 different cropping sequences of soybean [ (L.) Merr.], corn ( L.), and cotton ( L.) at the Research and Education Center at Milan, TN, and eight sequences of corn and soybean at the Middle Tennessee Research and Education Center, Spring Hill, TN. Sequences were repeated in 4-yr phases from 2002 to 2014. Split-block cover crop treatments consisted of winter wheat ( L.), hairy vetch ( Roth), poultry litter, and a fallow control. Soil C and nutrient fluxes were calculated at surface (0-5 cm) and subsurface (5-15 cm) layers during Years 0, 2, 4, 8, and 12. After 12 yr, weighted means (0-15 cm) of soil pH, P, K, Ca, Mg, total N, and C were greater under poultry litter-amended soils compared with cover crops ( < 0.05). In addition, continuous corn sequences resulted in greater soil K, N, and C concentrations than soybean-soybean-corn-corn rotations ( < 0.05). Poultry litter treatments were positively correlated with greater soil fertility levels, as well as higher crop yield and soil biodiversity. These results underscore linkages between manure additions and cropping sequences, within the nutrient cycling, soil health, and crop production continuum.

Switchgrass Compositional Variations Arising from Spatial Distribution and Legume Intercropping

ABSTRACT Due to genetic diversity within and among switchgrass (Panicum virgatum), there may be genotype x environment and management-induced differences among secondary cell walls. Consequently, two separate experiments were conducted to determine feedstock variance using near-infrared spectrometry (NIRS). One experiment tested legume-intercrops [red clover (RC; Trifolium pratense), crimson clover (CC; Trifolium incarnatum), hairy vetch (HV; Vicia villosa), and partridge pea (PP; Chamaechrista fasciculata)], nitrogen (N) fertilization (0, 67, and 135 kg-N ha−1), and location impacts on characteristics. The second one determined on-farm bale variance within and across locations. Clustering NIRS data indicated that chemical signatures differed among locations and N-levels, but less so among intercrops. Results suggest that homogeneity may vary within a region responsible for supplying biomass to a biorefinery. Thus, conversion efficiencies and enzymatic requirements for ethanol production may be affected. Consequently, legumes may displace inorganic-N with minimal compositional changes, whereas location and N-level influence feedstock quality and recalcitrance level to a greater extent.

Changes of Soil Microbial Population and Structure Under Short-term Application of an Organically Enhanced Nitrogen Fertilizer

Abstract Interest in the use of alternate fertilizers has increased during recent years to improve soil productivity. An organically enhanced N fertilizer, containing 14.9% N, 4.3% P2O5, 18.1% S, 0.6% Fe, and 8% organic C, and is produced from a sterilized organic additive extracted from municipal wastewater biosolids and chemical fertilizers was evaluated for its effects on soil microbial populations and abundances in 0- to 15-cm depth of of two silt loam soils located at Jackson and Grand Junction, Tennessee. This treatment was compared to conventional N fertilizers and zero N control under nonirrigated corn (Zea mays L.) from 2011 to 2013. Three N-applied treatments (organically enhanced N fertilizer, ammonium sulfate, urea/NPKZn briquette) at 128/170 kg ha−1 and the zero N control were imposed at each location. The organically enhanced N fertilizer decreased the relative abundance of arbuscular mycorrhizal fungi but increased that of general microbes relative to the zero N control and increased that of general microbes compared with NPKZn briquette 4 to 7 months after their applications at an N rate of 128 kg ha−1 for corn within 2 years of experimentation on a relatively infertile soil with low organic matter. Soil general microbes and arbuscular mycorrhizal fungi were the two sensitive indicators of soil microbial structure response to fertilization. However, effects of the organically enhanced N fertilizer on soil microbial populations were not noticeable after corn harvest. In conclusion, application of the organically enhanced N fertilizer has noticeable influence on soil microbial structure/abundance but not on populations on relatively infertile soils with low organic matter from a short-term perspective.

Long-Term Soil Organic Carbon Changes as Affected by Crop Rotation and Bio-covers in No-Till Crop Systems

Soil organic carbon (SOC) sequestration is a potential negative-feedback for climate-warming gases in agriculture. The rate of no-tillage SOC storage is not well known due to large temporal and spatial biogeochemical and management variations. Therefore our objective was to compare long-term SOC fluxes at a no-till field site in Milan, Tennessee on Oxyaquic Fragiudalfs, in a split-block design with four replications. The whole-block was cropping sequences of corn, soybeans, and cotton with split-block bio-cover treatments of: winter wheat, hairy vetch, poultry litter, and a fallow control. Soil carbon flux was calculated at soil surfaces (0–5 cm) for years-0, 2, 4, and 8. During the first 2 years, small annual losses occurred in carbon over all treatments (1.40 Mg ha−1). During this time, cotton sequences lost significantly more surface SOC than other rotations. However, by year-4, SOC began to stabilize. By year-8, sequences with high frequencies of soybean and with greater temporal complexity generally gained greater SOC levels at 0–5 cm. Also, poultry litter bio-cover gained more surface SOC compared to wheat, vetch and fallow covers. Across all sequences and bio-covers, SOC had increased 1.47 Mg ha−1 after 8 years from pre-experimental levels of 9.20 Mg ha−1; suggesting long-term beneficial effects on C storage under no-till and diverse cropping sequences.